Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Taxpasta parameters produce an error exit status of 2 during standardise part #509

Open
AndreaQ7 opened this issue Jul 18, 2024 · 5 comments
Labels
bug Something isn't working

Comments

@AndreaQ7
Copy link

AndreaQ7 commented Jul 18, 2024

Description of the bug

Hello everyone,
I am getting the following error during the taxpasta standardise function using the data from the tutorial age:

Execution cancelled -- Finishing pending tasks before exit
-[nf-core/taxprofiler] Pipeline completed with errors-
[84/f9989c] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:KRAKENTOOLS_COMBINEKREPORTS_C
ENTRIFUGE (2)` terminated with an error exit status (1) -- Error is ignored
[fd/db45c6] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:KRAKENTOOLS_COMBINEKREPORTS_C
ENTRIFUGE (1)` terminated with an error exit status (1) -- Error is ignored
ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE 
(kaiju|db3)'

Caused by:
  Process `NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE (kaiju|db3)` terminated 
with an error exit status (2)


Command executed:

  taxpasta standardise \
       \
       \
      ERX5474932_pe_db3.kaijutable.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE":
      taxpasta: $(taxpasta --version)
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  Usage: taxpasta standardise [OPTIONS] PROFILE
  Try 'taxpasta standardise -h' for help.
  ╭─ Error ─────────────────────────────────────────────────────────────────────────────────────────────────────
─╮
  │ Missing option '--profiler' / '-p'. Choose from:                                                            
 │
  │         bracken,                                                                                            
 │
  │         centrifuge,                                                                                         
 │
  │         diamond,                                                                                            
 │
  │         ganon,                                                                                              
 │
  │         kaiju,                                                                                              
 │
  │         kmcp,                                                                                               
 │
  │         kraken2,                                                                                            
 │
  │         krakenuniq,                                                                                         
 │
  │         megan6,                                                                                             
 │
  │         metaphlan,                                                                                          
 │
  │         motus                                                                                               
 │
  ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────
─╯
@AndreaQ7 AndreaQ7 added the bug Something isn't working label Jul 18, 2024
@Midnighter
Copy link
Collaborator

It looks like the kaiju profiler option is not set, for some reason...

@Midnighter
Copy link
Collaborator

@AndreaQ7 can you please provide the command that you used to start the pipeline and your database file?

@AndreaQ7
Copy link
Author

AndreaQ7 commented Jul 19, 2024

Yes of course, I followed the tutorial: https://nf-co.re/taxprofiler/1.1.8/docs/usage/usage/tutorials/d
So the databases are the ones called "test-db-centrifuge.tar.gz" and "test-db-kraken2.tar.gz" and the command line is the one reported in the tutorial

nextflow run nf-core/taxprofiler -r 1.1.0 -profile conda\
--input samplesheet.csv --databases database.csv --outdir ./results \
--perform_shortread_qc \
--perform_shortread_hostremoval --hostremoval_reference GCF_000819615.1_ViralProj14015_genomic.fna.gz \
--perform_runmerging --save_runmerged_reads \
--run_centrifuge --run_kaiju --run_kraken2 \
--run_profile_standardisation \
--max_cpus 2 --max_memory '6.GB'

@Midnighter
Copy link
Collaborator

I just ran the exact same command with the preparatory steps from the tutorial and it completes successfully... So I cannot reproduce your error. Can you please try again from the start? You could also run the latest version -r 1.1.8.

@jfy133
Copy link
Member

jfy133 commented Aug 8, 2024

I agree @AndreaQ7 please try with the most recent version of the pipeline. 1.1.0 is very old comparatively :D

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

3 participants